benchmark: Performance analysis of the extract_island_species() function Uses system.time() for timing for reasons explained here: https://radfordneal.wordpress.com/2014/02/02/inaccurate-results-from-microbenchmark/ # nolint

Description

Performance analysis of the extract_island_species() function Uses system.time() for timing for reasons explained here: https://radfordneal.wordpress.com/2014/02/02/inaccurate-results-from-microbenchmark/ # nolint

Usage

benchmark(
  phylod,
  tree_size_range,
  num_points,
  prob_on_island,
  prob_endemic,
  replicates,
  extraction_method,
  asr_method,
  tie_preference,
  log_scale = TRUE,
  parameter_index = NULL,
  verbose = FALSE
)

Value

Data frame

Arguments

phylod: A phylo4d object from the package phylobase containing phylogenetic and endemicity data for each species.
tree_size_range: Numeric vector of two elements, the first is the smallest tree size (number of tips) and the second is the largest tree size
num_points: Numeric determining how many points in the sequence of smallest tree size to largest tree size
prob_on_island: Numeric vector of each probability on island to use in the parameter space
prob_endemic: Numeric vector of each probability of an island species being endemic to use in the parameter space
replicates: Numeric determining the number of replicates to use to account for the stochasticity in sampling the species on the island and endemic species
extraction_method: A character string specifying whether the colonisation time extracted is the minimum time (min) (before the present), or the most probable time under ancestral state reconstruction (asr).
asr_method: A character string, either "parsimony" or "mk" determines whether a maximum parsimony or continuous-time markov model reconstructs the ancestral states at each node. See documentation in castor::asr_max_parsimony() or castor::asr_mk_model() in castor R package for details on the methods used.
tie_preference: Character string, either "island" or "mainland" to choose the most probable state at each node using the max.col() function. When a node has island presence and absence equally probable we need to decide whether that species should be considered on the island. To consider it on the island use ties.method = "last" in the max.col() function, if you consider it not on the island use ties.method = "first". Default is "island".
log_scale: A boolean determining whether the sequence of tree sizes are on a linear (FALSE) or log (TRUE) scale
parameter_index: Numeric determining which parameter set to use (i.e which row in the parameter space data frame), if this is NULL all parameter sets will be looped over
verbose: Boolean. States if intermediate results should be printed to console. Defaults to FALSE